R/PDBdataset.R

In judyheewonlee/BCB420.2019.PDB: BCB420.2019.PDB

#' PDBdataset.R
#'
#' \code{PDBdataset} Generates a PDB-HGNC mapping database linking HGNC transcripts
#' to PDB transcript identifiers. The resulting database also contains several
#' annotations about each transcript such as it's basic description and
#' PDB sequences.
#'
#' @export

PDBdataset <- function() {

  # Fetch Data from ensembl and retrieve a dataframe
  martDF <- getData()

  message("Building the database...")
  # Build the database
  myDB <- list()
  myDB <- addHGNC(myDB, martDF)
  myDB <- addTranscripts(myDB, martDF)

  message("Adding PDB chains...")
  myDB <- addpdbChain(myDB, martDF)

  message("Adding PDB IDS ...")
  myDB <- addPDB(myDB, martDF)
  myDB <- addPDBdata(myDB)

  message("Database successfully generated!")

  return(myDB)

}

# [END]